I can think of two problems, depending on what you are trying to place.
First, if you are trying to place a ground object, such a missile site, or almost any ground object, remember that relative to the size of the map they are very small. They may be the size of a pinhead, are maybe a white dot or smudge. So, zoom in before placing the object because they can be hard to locate if you do not.
Aircraft and moving moving vehicles are represented by large icons that remain the same size regardless of whether the map is zoomed in or not. To see what objects you have placed, click on the icons to the far right that have question marks over them. Doing so will list the icons.
Second, be aware of your filter setting that may be set not to include the item your are placing. If the filters have been set, you will not see it until you click on the correct filter, and there are five filters. I would expect that I covered your problem in the foregoing paragraph.
To get some good instruction on the mission builder, go here: http://tacops.virtualfightersquadrons.com/
There is no totally exhaustive instructions for the mission builder anywhere that I know of. But, reading the Jane's manual, the TSH section on new objects and creation of objects, the foregoing website and tidbits of information that you can pick up from this forum or the TSH forum, you can become quite proficient.
The mission builder is the heart and soul of the sim because it adds all of the interesting varieties of the experience of air combat. Dragon's missions are a blessing to the JF18 community becaus he produces them with great frequency by using, IMO, a method similar to mass production. He standardizes certain elements for a mission set so he can concentrate on introducing different elements and problems into each mission. That way, each mission is not created from scratch, at least as to certain components.
Shadow, Recluse and many others have produced wonderful missions and campaigns. You can download them from the VFA-41 website and from
the site I directed you to, above. TSH has made many missions and campaigns available that were authored by Dragon and many others. TSH has incorporated most, if not all, its missions into the JSGME system, and I am not sure how you convert them, if at all, with the .cmf extension to use them in TSH 3.06. Someone else can address that issue.
Good mission building is a tedious enterprise, but it can be very satisfying. It can take hours, literally days, to get the mission just right for your tastes. Once you get proficient at it, you can build variables into the mission so that each time you fly it you will face different challenges. A little knowledge of history, current events, geography and military technology will be a helpful tool, as well. Writing skills for briefing and de-briefing can make your mission more attractive, and, in the end, logical thinking when building the de-briefing for missions results is important.
Have at it.